Monday, October 26, 2009


Curiosity question: do the current DTC genomics companies report out copy number variations (CNVs) to their customers? Are any of their technologies unable to read these? Clearly Knome (or Illumina, which isn't DTC but sort of competing with them) should be able to get this info from the shotgun sequencing. But what about the array-based companies such as Navigenics & 23andMe? My impression is that any high density SNP array data can be mined for copy number info, but perhaps there are caveats or restrictions on that.

It would seem that with CNVs so hot in the literature and a number of complex diseases being associated to them, this would be something the DTC companies would jump at. But have they?


cariaso said...

not currently. The file formats returned by the companies do not readily support this. The Navigenics chip is particularly well suited for this.

while it would be nice to have this, most CNVs are well tagged by SNPs.

id said...

What kind of file format/data would be required to support CNV analysis ? Presumably intensities relative to some reference genome ?